To further study the statistical differences between isogenic iPSC lines, we grouped them based on the donor (T14, T42, T53, and T55) and performed SAM on the 1,000 most variably expressed genes across all PSC lines. This resulted in the identification of 167 differentially expressed genes between the isogenic iPSC groups from different donors (Table S6). Clustering of all samples according to these genes was visualized as an annotated heatmap (Figure 3A). Principal-component analysis (PCA) using this167-gene set confirmed donor-specific clustering (Figure S4C). Furthermore, when we annotated the DMCs by assigning them to the nearest transcription start site (TSS) (Table S7), we found that 29 of those 167 genes also overlapped with donor-specific DMCs. These DMCs were largely enriched in promoter regions (conventionally defined as ±1 kb from TSS), supporting the hypothesis that epigenetic differences reflect the transcriptional variation between iPSC lines derived from different donors (Figure 3B). qPCR analyses on selected genes (MEG3, WNT3A, SOX17, and SNAI2) replicated these results (Figure 3C). GO analysis of these 167 differentially expressed genes primarily indicated biological processes related to early development, which
